Differential Subnuclear Localization and Replication Timing of Histone H3 Lysine 9 Methylation States

Abstract

Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells

“…A possible explanation for these differences is that earlier studies used IP antibodies specific for histone H3K9Me2 in contrast to the present work, which focused on H3K9Me3. Thus, while histone H3K9Me2 and H3K9Me3 are dynamic intermediates of different methylated states they appear to mark very different functional chromatin domains Di-and trimethyl histone lysine 9 were found to reside as stable methylation states within different chromatin sites (Wu et al, 2005). Our study cannot provide further insights on this point as we did not carry out ChIP experiments using anti-H3K9Me2-specific antibodies.…”

CLLD8/KMT1F Is a Lysine Methyltransferase That Is Important for Chromosome Segregation

“…Interestingly, if SUV39h1 invalidation does not completely abrogate H3K9 trimethylation, it results in a more diffuse and modified pattern in mouse cells (26,27), and evidence from the literature favors the existence of different pathways for the trimethylation of H3K9 residues, especially at pericentromeres (28,29). Indeed, SETDB1/KMT1E, which is mainly involved in the regulation of euchromatic sequence and associates with corepressors at silenced promoters (29), was also found to modulate H3K9 trimethylation at pericentric heterochromatin and to interact with HP1 (30,31), suggesting that it may also contribute to heterochromatin formation.…”

“…Indeed, SETDB1/KMT1E, which is mainly involved in the regulation of euchromatic sequence and associates with corepressors at silenced promoters (29), was also found to modulate H3K9 trimethylation at pericentric heterochromatin and to interact with HP1 (30,31), suggesting that it may also contribute to heterochromatin formation. Thus, the mechanism by which KMT1F modulates histone methylation is currently unknown, but despite the fact that SUV39H, G9a, and KMT1F modify the same residue, they may also play unique roles in the distribution of H3K9me3 and/or involve different protein complexes or noncoding RNAs (28,31).…”

The expanding role of the Ehmt2/G9a complex in neurodevelopment

“…H3K9me2 has been shown to mark distinct sets of late replicating genes; upon Ehmt2 depletion however there is no effect on the replication timing of these genes. [80][81][82] Via its role in regulating H3K56 monomethylation, Ehmt2 plays a direct part in regulating the binding of Pcna to chromatin during late G1 to early S-phase. 3 Loss of Ehmt2 in mouse embryonic stem cells leads to a delay in progression through S-phase.…”